Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2022 Jun 6;3(7):885–898. doi: 10.1038/s43018-022-00391-0

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 4 — a, UMAP projection of scATAC-seq profiles colored by chromVAR TF motif bias-corrected deviations of the indicated TFs (NFKB1/2 and RELA/B were significantly enriched in C11_CD8 compared with the other CD8 T cell clusters; two-sided Wilcoxon rank-sum test P < 2.2 × 10⁻¹⁶, n = 18,736 cells). b, Violin plots of gene activity scores of the indicated NF-κB transcriptional targets for effector/nondysfunctional (C4,5,7_CD8) and dysfunctional (C8,9,10,11_CD8) T cell clusters. Pairwise comparisons of gene activity scores for the indicated gene between specified T cell clusters were determined using a two-sided Wilcoxon rank-sum test. The resulting P values underwent multi-test correction with the FDR method (**adjusted P < 0.01, ****adjusted-P < 0.0001; raw adjusted P values are listed in the source data; for clusters 4, 5, 7, 8, 9, 10, 11, n = 1,810, 1,821, 873, 924, 1,775, 2,440 and 1,613 cells, respectively). c, Violin plots showing gene expression levels of the indicated NF-κB transcriptional targets in CD4⁺ and CD8⁺ clusters, clustered as indicated in Fig. 3a (for clusters 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14, n = 8,677, 7,423, 5,390, 5,272, 4,469, 4,160, 3,974, 3,689, 1,080, 890, 751, 669, 618 and 328 cells, respectively). d, Flow cytometry analysis of tumor-infiltrating CD8⁺ T cells. UMAP projection of expression of selected T cell markers in CD8⁺ T cells (n = 9 ccRCC patients). Color gradient indicates expression level (red, high; blue, low). e, Protein expression of NF-κB targets in tumor-infiltrating CD8⁺ T cells. FACS plot (FAS versus TRAF1) overlay of PD-1⁻TOX⁻ (nondysfunctional) and PD-1⁺TOX⁺4-1BB⁺ (late dysfunctional) CD8⁺ T cell populations (left). Dot plots showing the percentages of FAS⁺ and FAS⁺TRAF1⁺ cells in different CD8⁺ T cell populations (right; one-way ANOVA test, Holm–Sidak correction for multiple comparisons; n = 9 ccRCC patients; **P < 0.01, ***P < 0.001, ****P < 0.0001; raw P values are listed in the source data). f, Apoptosis flow cytometry analysis. Bar graph showing the viability status (mean ± s.e.m.) as defined by flow cytometry for the indicated CD8⁺ T cell subsets (n = 10 ccRCC patients; raw P values are listed in the source data).

Source data